OK, first off I do not know how Combat Reporter works, so this is speculation based on how Intel Monkey works. There is only one archive folder, and if and only if the player uses the -archive switch, the game puts copies of all the report files into that folder and adds the game date to the name of each file. If you've been using the -archive switch then have a look in the archive folder and you will pretty quickly see how it is organized.
If Combat Reporter has the ability to load in multiple turns at once, then it definitely uses the archive folder because that is the only place where multiple turns of report files are found.
But going back to your original question, you had a sync bug, but got your opponent to send you the truthful combat report. You replaced the bad combat report with the good one. Then you told Combat Reporter to load that turn again, but it still shows the 'bad' combat results for that turn. That's how I understood what you wrote, put into my own words.
My suggestion is that you go into the archive folder and replace that copy of the day's combat report with the good one. If that doesn't make sense yet, then before you do anything else go and have a look at the archive folder, find the combat report named with the appropriate date, open (edit) it and see if it is the good copy or still the bad copy.